Table 5 COSMIC mutation analysis by considering genes related to PPIs predicted from best methods in our and PERA approaches and the relative amount of somatic and germline mutated genes

BLCA

ERBB3,NOTCH1,TSC1

–

BRCA

AKT1,ARID1A,BAP1,BRCA2,CCND1,CDH1,CDKN1B,

ERBB2,ESR1,NOTCH1,PIK3CA,RB1,TP53

BRCA2,CHEK2,RB1,TP53

AKT1,BRCA2,CCND1,CDH1,CDKN1B,ERBB2,ESR1,

BRCA2,CHEK2,TP53

GATA3,NOTCH1,PIK3CA,TP53

COAD

ERBB3

–

GBM

PIK3CA,PIK3R1

–

HNSC

ERBB3,MTOR,NOTCH1,TSC2

–

KIRC

MET,MTOR,NF2,TSC1,TSC2,VHL

MET,TSC1,TSC2,VHL

MET,MTOR,TSC1,TSC2,VHL

LGG

BRAF,EGFR,PTEN,RAF1,TP53

ATM,PTEN,TP53

LUAD

NOTCH1,RB1,TP53

RB1

–

–

LUSC

NOTCH1,RB1,TP53

RB1

TP53

–

OV

AKT1,ARID1A,BRAF,BRCA2,CCNE1,CTNNB1,ERBB2,

BRCA2,MSH2,MSH6,STK11

MAPK1,MSH2,PIK3R1

AKT1,BRAF,CCNE1,CTNNB1,ERBB2,MAPK1,PIK3R1

–

PRAD

AR,BRAF,NDRG1,PTEN,RAF1

PTEN

AR,BRAF,RAF1

–

READ

AKT1,BRAF,CTNNB1,MAP2K1,MSH2,MSH6,PIK3CA,

MSH2,MSH6

PIK3R1,SMAD3,SMAD4,SRC,TP53

AKT1,BRAF,CTNNB1,MAP2K1,PIK3CA,PIK3R1,SMAD3,SMAD4,SRC,TP53

–

SKCM

ERBB3,NOTCH1

–

STAD

BRAF,CDH1,ERBB2,ERBB3,PIK3CA

CDH1

THCA

BRAF,MTOR

CDKN1B

BRAF,NRAS

UCEC

MSH2,MTOR,PTEN,SRC

MSH2,MSH6,PTEN

MTOR,PTEN,SRC,YWHAE

PTEN